Tracing enteric pathogen contamination in sub-Saharan African groundwater

Quantitative PCR (qPCR) can rapidly screen for an array of faecally-derived bacteria, which can be employed as tracers to understand groundwater vulnerability to faecal contamination. A microbial DNA qPCR array was used to examine 45 bacterial targets, potentially relating to enteric pathogens, in 22 groundwater supplies beneath the city of Kabwe, Zambia in both the dry and subsequent wet season. Thermotolerant (faecal) coliforms, sanitary risks, and tryptophan-like fluorescence, an emerging real-time reagentless faecal indicator, were also concurrently investigated. There was evidence for the presence of enteric bacterial contamination, through the detection of species and group specific 16S rRNA gene fragments, in 72% of supplies where sufficient DNA was available for qPCR analysis. DNA from the opportunistic pathogen Citrobacter freundii was most prevalent (69% analysed samples), with Vibrio cholerae also perennially persistent in groundwater (41% analysed samples). DNA from other species such as Bifidobacterium longum and Arcobacter butzleri was more seasonally transient. Bacterial DNA markers were most common in shallow hand-dug wells in laterite/saprolite implicating rapid subsurface pathways and vulnerability to pollution at the surface. Boreholes into the underlying dolomites were also contaminated beneath the city highlighting that a laterite/saprolite overburden, as occurs across much of sub-Saharan aquifer, does not adequately protect underlying bedrock groundwater resources. Nevertheless, peri-urban boreholes all tested negative establishing there is limited subsurface lateral transport of enteric bacteria outside the city limits. Thermotolerant coliforms were present in 97% of sites contaminated with enteric bacterial DNA markers. Furthermore, tryptophan-like fluorescence was also demonstrated as an effective indicator and was in excess of 1.4 μg/L in all contaminated sites

Emerging contaminants in urban groundwater sources in Africa

The occurrence of emerging organic contaminants within the aquatic environment in Africa is currently unknown. This study provides early insights by characterising a broad range of emerging organic contaminants (n > 1000) in groundwater sources in Kabwe, Zambia. Groundwater samples were obtained during both the dry and wet seasons from a selection of deep boreholes and shallow wells completed within the bedrock and overlying superficial aquifers, respectively. Groundwater sources were distributed across the city to encompass peri-urban, lower cost housing, higher cost housing, and industrial land uses. The insect repellent DEET was ubiquitous within groundwater at concentrations up to 1.8 mg/L. Other compounds (n ¼ 26) were detected in less than 15% of the sources and included the bactericide triclosan (up to 0.03 mg/L), chlorination by-products e trihalomethanes (up to 50 mg/L), and the surfactant 2,4,7,9-tetramethyl-5-decyne-4,7-diol (up to 0.6 mg/L). Emerging contaminants were most prevalent in shallow wells sited in low cost housing areas. This is attributed to localised vulnerability associated with inadequate well protection, sanitation, and household waste disposal. The five-fold increase in median DEET concentration following the onset of the seasonal rains highlights that more mobile compounds can rapidly migrate from the surface to the aquifer suggesting the aquifer is more vulnerable than previously considered. Furthermore it suggests DEET is potentially useful as a wastewater tracer in Africa. There was a general absence of personal care products, life-style compounds, and pharmaceuticals which are commonly detected in the aquatic environment in the developed world. This perhaps reflects some degree of attenuation within the subsurface, but could also be a result of the current limited use of products containing emerging contaminants by locals due to unaffordability and unavailability. As development and population increases in Africa, it is likely a wider-range of emerging contaminants will be released into the environment

In-situ tryptophan-like fluorescence: a real-time indicator of faecal contamination in drinking water supplies

Enteric pathogens are typically inferred from the presence of surrogate indicator organisms such as thermo-tolerant (faecal) coliforms (TTCs). The analysis of TTCs requires time-consuming incubation in suitable laboratories, which can limit sampling resolution, particularly during critical pollution events. Here, we demonstrate the use of in-situ fluorimeters targeting tryptophan-like compounds as a rapid, reagentless indicator of TTCs in groundwater-derived potable water supplies in Africa. A range of other common indicators of TTCs were also determined including nitrate, turbidity, and sanitary risk survey scores. Sampling was conducted during both the dry and wet seasons to investigate seasonality. Tryptophan-like fluorescence was the most effective predictor of both presence/absence and number of TTCs during both seasons. Seasonal changes in tryptophan-like fluorescence in deeper supplies suggest it is transported more efficiently through the aquifer than TTCs. Moreover, the perennial elevated concentrations in some wells suggest it is more resilient than TTCs in groundwater. Therefore tryptophan-like fluorescence could also be a better indicator of some smaller, more easily transported, and long-lived, pathogenic enteric viruses. These sensors have the potential to be included in real-time pollutionalert systems for drinking water supplies throughout the world, as well as for mapping enteric pathogen risks in developing regions

Impact of organizational factors on adherence to laboratory testing protocols in adult HIV care in Lusaka, Zambia

Background Previous operational research studies have demonstrated the feasibility of large-scale public sector ART programs in resource-limited settings. However, organizational and structural determinants of quality of care have not been studied. Methods We estimate multivariate regression models using data from 13 urban HIV treatment facilities in Zambia to assess the impact of structural determinants on health workers’ adherence to national guidelines for conducting laboratory tests such as CD4, hemoglobin and liver function and WHO staging during initial and follow-up visits as part of Zambian HIV care and treatment program. Results CD4 tests were more routinely ordered during initial history and physical (IHP) than follow-up (FUP) visits (93.0 % vs. 85.5 %; p < 0.01). More physical space, higher staff turnover and greater facility experience with ART was associated with greater odds of conducting tests. Higher staff experience decreased the odds of conducting CD4 tests in FUP (OR 0.93; p < 0.05) and WHO staging in IHP visit (OR 0.90; p < 0.05) but increased the odds of conducting hemoglobin test in IHP visit (OR 1.05; p < 0.05). Higher staff burnout increased the odds of conducting CD4 test during FUP (OR 1.14; p < 0.05) but decreased the odds of conducting hemoglobin test in IHP visit (0.77; p < 0.05) and CD4 test in IHP visit (OR 0.78; p < 0.05). Conclusion Physical space plays an important role in ensuring high quality care in resource-limited setting. In the context of protocolized care, new staff members are likely to be more diligent in following the protocol verbatim rather than relying on memory and experience thereby improving adherence. Future studies should use prospective data to confirm the findings reported here

Applying in-situ fluorescence and molecular screening techniques to understand contamination and contributing risk factors in shallow urban groundwaters in sub-Saharan Africa

Shallow hand dug wells and boreholes are particularly important as local sources of water in sub-Saharan Africa. They are also potentially most at risk from anthropogenic contamination. As such, mapping groundwater contamination and understanding the key risk factors remains a priority. The risk of microbial contamination is often evaluated using sanitary risk assessments and characterised using thermotolerant coliforms and faecal streptococci as indicators. This paper evaluates this approach along with novel techniques including molecular pathogen screening and in-situ optical fluorescence for tryptophan (a protein waste water marker), as well as traditional chemical indicators. Groundwater quality sampling and characterisation were done during the wet and dry seasons at 50 sites (including hand dug wells and boreholes) across Kabwe, Zambia. Kabwe is a former mining town in Central province with a history of contamination and a population of around 200,000, which is largely dependent on groundwater for water supply

One Hundred Priority Questions for the Development of Sustainable Food Systems in Sub-Saharan Africa

Sub-Saharan Africa is facing an expected doubling of human population and tripling of food demand over the next quarter century, posing a range of severe environmental, political, and socio-economic challenges. In some cases, key Sustainable Development Goals (SDGs) are in direct conflict, raising difficult policy and funding decisions, particularly in relation to trade-offs between food production, social inequality, and ecosystem health. In this study, we used a horizon-scanning approach to identify 100 practical or research-focused questions that, if answered, would have the greatest positive impact on addressing these trade-offs and ensuring future productivity and resilience of food-production systems across sub-Saharan Africa. Through direct canvassing of opinions, we obtained 1339 questions from 331 experts based in 55 countries. We then used online voting and participatory workshops to produce a final list of 100 questions divided into 12 thematic sections spanning topics from gender inequality to technological adoption and climate change. Using data on the background of respondents, we show that perspectives and priorities can vary, but they are largely consistent across different professional and geographical contexts. We hope these questions provide a template for establishing new research directions and prioritising funding decisions in sub-Saharan Africa

One hundred priority questions for the development of sustainable food systems in sub-Saharan Africa

Sub-Saharan Africa is facing an expected doubling of human population and tripling of food demand over the next quarter century, posing a range of severe environmental, political, and socio-economic challenges. In some cases, key Sustainable Development Goals (SDGs) are in direct conflict, raising difficult policy and funding decisions, particularly in relation to trade-offs between food production, social inequality, and ecosystem health. In this study, we used a horizon-scanning approach to identify 100 practical or research-focused questions that, if answered, would have the greatest positive impact on addressing these trade-offs and ensuring future productivity and resilience of food-production systems across sub-Saharan Africa. Through direct canvassing of opinions, we obtained 1339 questions from 331 experts based in 55 countries. We then used online voting and participatory workshops to produce a final list of 100 questions divided into 12 thematic sections spanning topics from gender inequality to technological adoption and climate change. Using data on the background of respondents, we show that perspectives and priorities can vary, but they are largely consistent across different professional and geographical contexts. We hope these questions provide a template for establishing new research directions and prioritising funding decisions in sub-Saharan Africa

AVONET: morphological, ecological and geographical data for all birds

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species‐level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity

Impact of organizational factors on adherence to laboratory testing protocols in adult HIV care in Lusaka, Zambia

Abstract Background Previous operational research studies have demonstrated the feasibility of large-scale public sector ART programs in resource-limited settings. However, organizational and structural determinants of quality of care have not been studied. Methods We estimate multivariate regression models using data from 13 urban HIV treatment facilities in Zambia to assess the impact of structural determinants on health workers’ adherence to national guidelines for conducting laboratory tests such as CD4, hemoglobin and liver function and WHO staging during initial and follow-up visits as part of Zambian HIV care and treatment program. Results CD4 tests were more routinely ordered during initial history and physical (IHP) than follow-up (FUP) visits (93.0 % vs. 85.5 %; p  Conclusion Physical space plays an important role in ensuring high quality care in resource-limited setting. In the context of protocolized care, new staff members are likely to be more diligent in following the protocol verbatim rather than relying on memory and experience thereby improving adherence. Future studies should use prospective data to confirm the findings reported here.</p